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PubMed1984

Promoter selectivity of Escherichia coli RNA polymerase. II: Altered promoter selection by mutant holoenzymes.

Using the in vitro mixed transcription system (Kajitani and Ishihama (1983a, 1983b), we examined selective transcription of truncated DNA templates carrying lac(UV5), rrnE or rpsA promoters by RNA polymerase holoenzymes from pairs of wild-type parents and mutants with a mutation in one or more RNA polymerase subunit genes. The promoter selectivity of RNA polymerases from two sigma-subunit mutants carrying either rpoD2 or rpoD285 differed markedly from that of the respective wild-type enzymes. Both the parental RNA polymerases, however, exhibited abnormal promoter selectivity compared with holoenzymes from various wild-type E. coli strains. On the other hand, all the RNA polymerases from rpoB and/or rpoC mutants and the respective wild-type parents were similar, if not identical, in promoter selection at low temperature. At high temperature, however, RNA polymerases from mutants carrying rpoB2B7 and rpoC4, affecting the beta and beta' subunits, respectively, showed decreased transcription from the high-affinity slow-transcribable promoter rrnEp2 whereas the rpoC92 and rpoB906 X rpoC907 mutant enzymes both lost transcription activity from the strong promoter lacP(UV5). Taking all these observations together we conclude that not only the sigma subunit but also the beta and beta' subunits are involved in the recognition of promoters.

DNA-Directed RNA Polymerases↗
PubMed1991

RNA polymerase bound to the PR promoter of bacteriophage lambda inhibits open complex formation at the divergently transcribed PRM promoter. Implications for an indirect mechanism of transcriptional activation by lambda repressor.

We demonstrate that RNA polymerase bound at the PR promoter of bacteriophage lambda can repress transcription initiation from the divergently transcribed PRM promoter in vitro. Using abortive initiation and run-off transcription experiments we show that inactivating mutations introduced into either the -10 or -35 regions of PR result in a significant increase in the rate of formation of transcriptionally competent complexes at the PRM promoter. This is due primarily to an increase in the rate constant for the isomerization of closed to open complexes. Gel shift and DNase I footprinting experiments were employed to further define the mechanism by which PR sequences mediate PRM repression. From these assays we were able to conclude that the formation of an open complex at the PR promoter did not exclude RNA polymerase from binding at PRM. Rather, initiation at PRM was impaired because closed complexes must isomerize in the presence of an open complex already situated at the PR promoter. Extensive evidence has been obtained previously indicating that lambda repressor activates transcription directly by contacting RNA polymerase situated at the PRM promoter. Results presented here raise the possibility that an additional mechanism could be operative, whereby lambda repressor indirectly activates PRM transcription by excluding RNA polymerase from the PR promoter.

Bacteriophage lambda↗
PubMed1983

The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter.

Fractionation of HeLa cell extracts reveals the presence of a promoter-specific transcription factor, Sp 1, which activates a class of promoters that includes the SV40 early promoter but not several others that have been tested. We analyzed SV40 early-promoter deletion mutants and determined that transcriptional activation by Sp 1 requires sequences within tandem 21 bp repeats located 70-110 bp upstream of the transcription initiation sites. In a DNAase footprinting assay, Sp 1 protected sequences in this same 21 bp repeat region, thus indicating the presence of a specific site for Sp 1 binding. During purification of Sp 1, there was a correlation between transcription-stimulatory activity and promoter-binding activity. These results suggest that direct binding of Sp 1 to sequences in the upstream promoter element is the mechanism by which this factor activates transcription by RNA polymerase II at the SV40 early promoter.

Binding Sites↗
PubMed1985

12-O-tetradecanoylphorbol-13-acetate promotes tumors prior to initiation in two-stage promotion.

The tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) and the non-promoter mezerein both induce ornithine decarboxylase activity in mouse epidermis by a route which can be blocked by indomethacin. In two-stage tumor promotion experiments in mice with mezerein as the stage II promoter, TPA was effective as the stage I promoter whether it was applied before or after an initiating dose of 7,12-dimethylbenz[a]anthracene (DMBA). There appear to be at least 4 events in promotion, only 3 of which are caused by second stage promoters.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1982

Construction and characterization of E. coli promoter-probe plasmid vectors. III. pBR322 derivatives with deletions in the tetracycline resistance promoter region.

Deletions of the promoter region for the tetracycline-resistance (Tcr) gene(s) of pBR322 were constructed in order to generate new promoter-probe plasmid cloning vectors. The deletions were constructed in vitro by exonuclease digestion at the HindIII site and blunt-end ligation of the digestion products. Plasmids which lost the HindIII site but retained the EcoRI site carried deletions ranging from 5 to 60 bp. Some of the plasmids lacked the nucleotide sequences required for initiation of transcription from the Tcr promoter and "anti-Tcr" promoter. Three of the promoter-deletion plasmids (containing deletions of 5-29 bp) formed tight-binding complexes with RNA polymerase in vitro, despite their tetracycline sensitive phenotype. One deletion plasmid, pPV33, retained three out-of-phase stop codons located between the promoter-cloning site (EcoRI) and the translational start codon for the tetracycline resistance gene. These features give pPV33 several advantages over previously described promoter-cloning vehicles.

Cloning, Molecular↗
PubMed1993

Studies on liver tumor promotion in the rat by orotic acid: dose and minimum exposure time required for dietary orotic acid to promote hepatocarcinogenesis.

Our earlier studies indicated that orotic acid, a precursor for pyrimidine nucleotide biosynthesis, exerts a promoting effect on rat hepatocarcinogenesis. The present study was designed to determine the optimum conditions of exposure to orotic acid required for promotion of hepatocarcinogenesis in the initiated rats. The first series of experiments was designed to determine the optimum dose of orotic acid needed to exert its liver tumor promoting effect. Accordingly male Fischer rats were given diethylnitrosamine (200 mg/kg, i.p.) or 0.9% NaCl. One week later carcinogen-injected rats were divided into six groups and fed either basal diet or the same diet containing 0.1, 0.5, 1, 2 or 4% orotic acid. Rats given 0.9% NaCl were fed 4% orotic acid. Two-thirds partial hepatectomy was performed on all animals 10 weeks after starting on their respective diets, and all groups were killed 3 weeks thereafter. Analysis of gamma-glutamyltransferase-positive foci and nodules revealed that 0.5-1% orotic acid in the diet is sufficient to exert a significant promoting effect on the selective growth of initiated hepatocytes, while higher concentrations of orotic acid were only marginally more effective. No gamma-glutamyltransferase-positive foci were observed in animals given 4% orotic acid diet following saline injection. Using 1% orotic acid as the promoting regimen, in the next series, the minimum exposure time required for dietary orotic acid to promote liver carcinogenesis was determined. Male Fischer 344 rats were given i.p. either 1,2-dimethylhydrazine dihydrochloride (100 mg/kg) or 0.9% NaCl 18 h after 2/3 partial hepatectomy. After 1 week of recovery one group of rats was continued on a semisynthetic basal diet, while others were transferred to the same basal diet containing 1% orotic acid. Rats that were on the 1% orotic acid diet were progressively transferred to the basal diet after 5, 10, 20, 29 and 40 weeks of exposure. All rats were sacrificed 54 weeks after the beginning of the experiment. The results indicate that 100% of the initiated rats developed hepatic nodules whether or not they were exposed to an orotic acid-containing diet. However, the incidence of hepatocellular carcinoma was greatly increased in animals exposed to the orotic acid diet, with 42% incidence in initiated rats given orotic acid diet for 10 weeks and up to 75% in those exposed to this diet for 40 weeks. Further, promotion by orotic acid exhibited a high metastatic potential with 33-60% metastasis to the lungs.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1999

Anti-tumor-promoting activity of a polyphenolic fraction isolated from grape seeds in the mouse skin two-stage initiation-promotion protocol and identification of procyanidin B5-3'-gallate as the most effective antioxidant constituent.

Procyanidins present in grape seeds are known to exert anti-inflammatory, anti-arthritic and anti-allergic activities, prevent skin aging, scavenge oxygen free radicals and inhibit UV radiation-induced peroxidation activity. Since most of these events are associated with the tumor promotion stage of carcinogenesis, these studies suggest that grape seed polyphenols and the procyanidins present therein could be anticarcinogenic and/or anti-tumor-promoting agents. Therefore, we assessed the anti-tumor-promoting effect of a polyphenolic fraction isolated from grape seeds (GSP) employing the 7,12-dimethylbenz[a]anthracene (DMBA)-initiated and 12-O-tetradecanoylphorbol 13-acetate (TPA)-promoted SENCAR mouse skin two-stage carcinogenesis protocol as a model system. Following tumor initiation with DMBA, topical application of GSP at doses of 0.5 and 1.5 mg/mouse/application to the dorsal initiated mouse skin resulted in a highly significant inhibition of TPA tumor promotion. The observed anti-tumor-promoting effects of GSP were dose dependent and were evident in terms of a reduction in tumor incidence (35 and 60% inhibition), tumor multiplicity (61 and 83% inhibition) and tumor volume (67 and 87% inhibition) at both 0.5 and 1.5 mg GSP, respectively. Based on these results, we directed our efforts to separate and identify the individual polyphenols present in GSP and assess their antioxidant activity in terms of inhibition of epidermal lipid peroxidation. Employing HPLC followed by comparison with authentic standards for retention times in HPLC profiles, physiochemical properties and spectral analysis, nine individual polyphenols were identified as catechin, epicatechin, procyanidins B1-B5 and C1 and procyanidin B5-3'-gallate. Five of these individual polyphenols with evident structural differences, namely catechin, procyanidin B2, procyanidin B5, procyanidin C1 and procyanidin B5-3'-gallate, were assessed for antioxidant activity. All of them significantly inhibited epidermal lipid peroxidation, albeit to different levels. A structure-activity relationship study showed that with an increase in the degree of polymerization in polyphenol structure, the inhibitory potential towards lipid peroxidation increased. In addition, the position of linkage between inter-flavan units also influences lipid peroxidation activity; procyanidin isomers with a 4-6 linkage showed stronger inhibitory activity than isomers with a 4-8 linkage. A sharp increase in the inhibition of epidermal lipid peroxidation was also evident when a gallate group was linked at the 3'-hydroxy position of a procyanidin dimer. Procyanidin B5-3'-gallate showed the most potent antioxidant activity with an IC(50) of 20 microM in an epidermal lipid peroxidation assay. Taken together, for the first time these results show that grape seed polyphenols possess high anti-tumor-promoting activity due to the strong antioxidant effect of procyanidins present therein. In summary, grape seed polyphenols in general, and procyanidin B5-3'-gallate in particular, should be studied in more detail to be developed as cancer chemopreventive and/or anticarcinogenic agents.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1987

Elevated expression and point mutation of the Ha-ras proto-oncogene in mouse skin tumors promoted by benzoyl peroxide and other promoting agents.

The two-stage skin carcinogenesis model of initiation and promotion in SENCAR mice has been used to examine the effects of various tumor-promoting agents on the expression of the Ha-ras oncogene in early stages of tumorigenesis in vivo. Papillomas were induced in 7,12-dimethylbenz[a]anthracene (DMBA)-initiated SENCAR mouse epidermis by (i) complete promotion with benzoyl peroxide; (ii) complete promotion with 12-O-tetradecanoyl phorbol-13-acetate (TPA); and (iii) two-stage promotion with TPA for 2 weeks followed by mezerein for 9 weeks. Results of Northern blot hybridization analyses show that early papillomas contain significantly elevated levels of Ha-ras polyadenylated [poly(A)+] RNA, irrespective of the type of tumor promotion regimen used. This pattern holds for promoters of the phorbol ester class as well as for the free radical generating agent benzoyl peroxide. Furthermore, digestion of tumor DNA with diagnostic restriction endonucleases demonstrated that 9-week-old papillomas induced by DMBA contained a point mutation in the 61st codon of one allele of the Ha-ras gene. The results represent the earliest stage in the development of a papilloma at which a Ha-ras point mutation has been reported.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1984

Mutational dissection of the 21 bp repeat region of the SV40 early promoter reveals that it contains overlapping elements of the early-early and late-early promoters.

Using quantitative S1 nuclease analysis and recombinants which contain the SV40 early promoter region linked to the rabbit beta-globin gene coding sequence, we have studied the effect of deletion, inversion and point mutations, located within the 21 bp repeat region, on initiation of transcription from the early-early and late-early startsites in the absence of T-antigen. Our data establish unequivocally that the six GC-rich repeats present in the 21 bp repeat region are essential elements of both the early-early and late-early promoters and that they are not redundant, since mutations, which affect only the GC-rich repeat most proximal to the TATA box, decrease drastically the activity of the early-early promoter, but increase that of the late-early promoter. On the other hand, the four GC-rich repeats most proximal to the 72 bp repeat are common elements of the two overlapping early-early and late-early promoters. Our results, which confirm that the early-early promoter is stronger than the late-early one, also support our previous suggestion that they are in competition for the transcriptional machinery. The general organization of the SV40 early promoter region is discussed.

Base Composition↗
PubMed1980

Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant.

Using the promotor-cloning vehicle described by An and Friesen (J. Bacteriol. 140:400-410, 1979), Escherichia coli chromosomal deoxyribonucleic acid fragments derived from the lambda drifd18 transducing phage were cloned in one of several unique restriction endonuclease sites adjacent to tetracycline(tet) genes that lack their own promotor. One of these plasmids has been used to isolate nine variants having mutations that lie in a putative internal promoter which is located between rplL and rpoB. Deoxyribonucleic acid sequence analysis revealed that, in all nine mutants, a single base change, C to T, in the ribonucleic acid polymerase recognition site led to a large increase in promoter activity. Analysis of a variety of plasmids in which tet is fused to various promoters yielded the following results: (i) rplK and rplA, genes for ribosomal protein L11 and L1, respectively, were cotranscribed from a common promoter located upstream from rplK; (ii) there was a strong promoter in the region between the rplKA operon and rplJ, the gene for ribosomal protein L10; (iii) an attenuator region was located between rplL, the gene for ribosomal protein L12, and rpoB, the gene for ribonucleic acid polymerase subunit beta; (iv) transcription terminated immediately after rpoC, the gene for ribonucleic acid polymerase subunit beta'; (v) a gene coding for unknown protein U, which is located between tufB and the rplKA operon, had its own promoter; (vi) the tufB gene was separated from all of the genes described above and had its own promoter.

Bacterial Proteins↗
PubMedDate not supplied

In vitro assay for tumor promoters and anti-promoters.

Tumor promoters and anti-promoters have been shown to modify the induction of ornithine decarboxylase, the production of plasminogen activator, and the recovery of induced mutations. Data were presented to show that the recovery of mutagen-induced ouabain-resistant mutations in cultured Chinese hamster cells is increased with a tumor-promoter treatment and reduced by anti-promoter treatments. The results suggest that many induced mutations can either be repressed or derepressed by promoters or anti-promoters. The results also support the hypothesis that tumor initiation is due to a mutagenic event, while tumor promotion is the result of an epigenetic process involving cyclic nucleotide modulation of gene expression.

Animals↗
PubMed1982

Molecular mechanism of promoter selection in gene transcription. II. Kinetic evidence for promoter search by a one-dimensional diffusion of RNA polymerase molecule along the DNA template.

The rapid mixing-photocrosslinking technique, in conjunction with an immunoprecipitation assay developed to measure the change in the distribution of Escherichia coli RNA polymerase molecules bound to T7 DNA, has been applied to investigate the molecular mechanism of promoter search by RNA polymerase. The binding of RNA polymerase to the DNA template can be divided into at least two steps. The initial binding is rapid and occurs at nonspecific sites randomly distributed throughout the DNA molecule. This is followed by a relatively slow promoter search in which RNA polymerase is transferred from nonspecific sites to promoter sites through a series of intramolecular processes. The rate of polymerase loss from a segment of DNA which does not contain promoter sites is a function of the distance from this segment to both the promoter sites and the ends of the DNA molecule. The kinetic data are consistent with a molecular mechanism in which RNA polymerase undergoes a bidirectional linear diffusion along the DNA template to search for the promoter site. This interpretation is supported by the computer simulation which correctly predicts the relative rates of polymerase loss from various DNA segments. The mechanism derived from these studies is in accordance with the notion that the whole DNA molecule serves as an effective sink for trapping and guiding polymerase molecules during promoter search.

DNA, Viral↗
PubMed1998

Fed-batch cultivation of an oxygen-dependent inducible promoter system, the nar promoter in Escherichia coli with an inactivated nar operon.

The nar promoter of Escherichia coli is maximally induced under anaerobic or microaerobic conditions in the presence of nitrate. We previously demonstrated in batch experiments that the intact nar promoter of E. coli cloned into a pBR322-based plasmid serves as a high-level expression system in a nar mutant of E. coli (Lee et al., 1996b). In this study, we extend characterization of the nar promoter expression system to the fed-batch culture mode, which is widely used in industrial-scale fermentation. From these experiments, it was found that the specific beta-galactosidase activity expressed from the lacZ gene fused to the nar promoter was maximal when host cells were grown under aerobic conditions [dissolved oxygen, (DO) = 80%] to absorbance at 600 nm (OD600) = 35 before induction of the nar promoter by lowering DO to 1-2% with alternating microaerobic and aerobic conditions. Approximately 15 h after induction, the OD600 of the culture reached 135 and the specific beta-galactosidase activity increased to 40,000 Miller units, equivalent to approximately 35% of the total cellular proteins. The specific beta-galactosidase activity before induction was approximately 1,000 Miller units, giving an induction ratio of approximately 40. Based on these results, we conclude that the nar promoter provides a convenient and effective high level expression system under conditions of fed-batch culture.

Cell Culture Techniques↗
PubMed1999

Two control elements in the hepatitis B virus S-promoter are important for full promoter activity mediated by CCAAT-binding factor.

Natural occurring mutations in the preS-region are frequently found during chronic hepatitis B virus (HBV) infection. Here we used the mutated preS-region from a patient to study the transcriptional regulation of the S-promoter. The mutations were a CCAAT-box (MUT1) point mutation, a 6-base pair (bp) deletion (MUT2) 3' of the CCAAT-box, and a 153 bp deletion (MUT3) in the preS2 genome. Transfection experiments revealed for MUT1 and 2 30% to 40% and MUT3 75% of the wildtype (wt) S-promoter activity. In electro-mobility shift assays experiments, binding of a nuclear protein was impaired with MUT1. Ultraviolet cross-linking, South-Western, and gel shift experiments revealed a 30- to 40-kd protein interacting with the wt CCAAT-motif. Computer-assisted analysis and supershift experiments showed that CCAAT-binding factor (CBF) is the CCAAT-box binding protein. Cotransfection experiments with expression vectors for dominant-negative CBF or wt CBF showed that the wt S-promoter but not MUT1 could be regulated through CBF. Additionally, the CBF constructs did not modulate the basal activity of MUT2 but changes the activity of MUT3 like wt HBV. Artificial mutations were introduced in the MUT2 reporter constructs. Transfection experiments revealed that wt promoter activity could not be reconstituted. Therefore these experiments indicated the sterical position of CBF being essential for full S-promoter activity. Our study shows that the CCAAT-box and a second region is essential to mediate full S-promoter activity dependent on CBF. As these mutations also lead to retention of S-protein in the endoplasmic reticulum our results indicate that mutational changes in the preS-region might be linked to the progression of HBV-related liver disease.

CCAAT-Enhancer-Binding Proteins↗
PubMed1985

Mutational analysis of the maize chloroplast ATPase-beta subunit gene promoter: the isolation of promoter mutants in E. coli and their characterization in a chloroplast in vitro transcription system.

This paper describes the use of Escherichia coli to isolate Bal31 deletion mutants and single-base substitution mutants that functionally define the promoter of the maize chloroplast beta-ATPase gene (atpB). Promoter function in E. coli and in a chloroplast in vitro transcription system was determined by S1 nuclease protection experiments using RNA products from each mutant. The results show that in vitro the chloroplast RNA polymerase responds to the promoter point mutations in a quantitatively similar fashion to the E. coli RNA polymerase. Deletion analysis demonstrates that sequences 5' of the -35 region are not necessary for chloroplast promoter function in vitro and that the presence of an adjacent promoter drastically decreases the transcriptional activity of the atpB promoter in E. coli.

Adenosine Triphosphatases↗
PubMed1991

Properties of promoter regions of mdg1 Drosophila retrotransposon indicate that it belongs to a specific class of promoters.

A sequence 30 bp downstream from the start site of the Drosophila melanogaster retrotransposon mdg1 is shown to be responsible for correct and precise initiation of mdg1 RNA synthesis in combination with the RNA start-site sequence TCAGTT. A sequence-specific DNA binding protein is demonstrated to interact with the +30 sequence, and the efficient binding of this factor is necessary for in vivo transcriptional activity of the plasmid constructs containing mdg1 promoter fragments. The nucleotides -8/+34 of mdg1 represent a minimal promoter which is able to provide correct initiation of transcription by RNA polymerase II at basal levels. A comparison with properties of some other retrotransposable elements and several developmentally regulated cellular genes allows us to conclude that together they form a specific class of RNA polymerase II promoter. This promoter class characteristically lacks upstream sequences necessary for transcription initiation, such as TATA boxes, but requires a specific downstream promoter element within 40 bp downstream of the RNA start site. The level of transcription can, however, be modulated by upstream regulatory elements. The identified sequence-specific downstream initiation factor may be responsible for transcription initiation on promoters of some genes which belong to this class.

Animals↗
PubMed1995

RNA polymerase alpha subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes.

The ada and aidB genes are part of the adaptive response to DNA methylation damage in Escherichia coli. Transcription of the ada and the aidB genes is triggered by binding of the methylated Ada protein (meAda) to a specific sequence located 40-60 base pairs upstream of the transcriptional start, which is internal to an A/T-rich region. In this report we demonstrate that the Ada binding site is also a binding site for RNA polymerase. RNA polymerase is able to bind the -40 to -60 region of the ada and the aidB promoters in the absence of meAda, and its binding is mediated by the alpha subunit. This region resembles the UP element of the rrnB P1 promoter in location, sequence and mechanism of interaction with RNA polymerase. We discuss the function of UP-like elements in positively controlled promoters and provide evidence that Ada does not act by enhancing RNA polymerase binding affinity to the promoter region. Instead, Ada stimulates transcription by modifying the nature of the RNA polymerase-promoter interaction, allowing RNA polymerase to recognize the core promoter -35 and -10 elements in addition to the UP-like element.

Bacterial Proteins↗
PubMed1998

Testing promoter activity in the trypanosome genome: isolation of a metacyclic-type VSG promoter, and unexpected insights into RNA polymerase II transcription.

In trypanosomes, most genes are arranged in polycistronic transcription units. Individual mRNAs are generated by 5'-trans splicing and 3' polyadenylation. Remarkably, no regulation of RNA polymerase II transcription has been detected although many RNAs are differentially expressed during kinetoplastid life cycles. Demonstration of specific class II promoters is complicated by the difficulty in distinguishing between genuine promoter activity and stimulation of trans splicing. Using vectors that were designed to allow the detection of low promoter activities in a transcriptionally silent chromosomal context, we isolated a novel trypanosome RNA polymerase I promoter. We were however unable to detect class II promoter activity in any tested DNA fragment. We also integrated genes which were preceded by a T3 promoter into the genome of cells expressing bacteriophage T3 polymerase: surprisingly, transcription was alpha-amanitin sensitive. One possible interpretation of these results is that in trypanosomes, RNA polymerase II initiation is favored by genomic accessibility and double-strand melting.

Animals↗